Multiple sequence alignment - TraesCS3D01G280800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G280800 chr3D 100.000 2721 0 0 1 2721 388536927 388539647 0.000000e+00 5025
1 TraesCS3D01G280800 chr3D 95.484 310 14 0 2 311 605967905 605967596 1.880000e-136 496
2 TraesCS3D01G280800 chr3B 93.130 2431 153 6 305 2721 217385474 217383044 0.000000e+00 3552
3 TraesCS3D01G280800 chr3B 92.661 2330 150 8 305 2620 217314513 217312191 0.000000e+00 3336
4 TraesCS3D01G280800 chr3B 90.132 831 72 6 1891 2721 453196597 453197417 0.000000e+00 1072
5 TraesCS3D01G280800 chr3B 91.457 714 49 5 1953 2654 173224481 173225194 0.000000e+00 970
6 TraesCS3D01G280800 chr5D 93.543 2385 138 8 310 2684 362181108 362178730 0.000000e+00 3537
7 TraesCS3D01G280800 chr5D 95.484 310 14 0 2 311 447759481 447759172 1.880000e-136 496
8 TraesCS3D01G280800 chr5D 94.231 312 17 1 1 311 403620908 403620597 2.450000e-130 475
9 TraesCS3D01G280800 chr2D 92.651 2422 162 8 311 2720 315433792 315436209 0.000000e+00 3472
10 TraesCS3D01G280800 chr7D 93.774 2313 130 7 310 2615 579951048 579953353 0.000000e+00 3461
11 TraesCS3D01G280800 chr7D 94.534 311 17 0 1 311 167580302 167580612 5.270000e-132 481
12 TraesCS3D01G280800 chr7D 94.534 311 17 0 1 311 203189903 203189593 5.270000e-132 481
13 TraesCS3D01G280800 chr6D 92.571 2423 154 9 310 2721 380044446 380046853 0.000000e+00 3454
14 TraesCS3D01G280800 chr6D 94.212 311 18 0 1 311 8677809 8678119 2.450000e-130 475
15 TraesCS3D01G280800 chr5B 92.257 2428 164 14 310 2719 34275027 34272606 0.000000e+00 3421
16 TraesCS3D01G280800 chr1D 91.990 2422 167 17 310 2717 407177451 407179859 0.000000e+00 3373
17 TraesCS3D01G280800 chr1D 89.715 2421 233 12 311 2721 465924262 465921848 0.000000e+00 3077
18 TraesCS3D01G280800 chr2B 91.491 2421 192 8 305 2712 730047217 730044798 0.000000e+00 3317
19 TraesCS3D01G280800 chr1A 94.112 2140 120 1 311 2444 535101801 535099662 0.000000e+00 3249
20 TraesCS3D01G280800 chr1A 81.980 505 78 9 2226 2721 259891493 259891993 1.510000e-112 416
21 TraesCS3D01G280800 chr7B 89.311 2423 239 13 305 2712 685959927 685957510 0.000000e+00 3022
22 TraesCS3D01G280800 chr7B 94.212 311 18 0 1 311 648021298 648020988 2.450000e-130 475
23 TraesCS3D01G280800 chr1B 94.839 310 16 0 2 311 672832082 672832391 4.070000e-133 484
24 TraesCS3D01G280800 chr4D 94.212 311 18 0 1 311 445342804 445343114 2.450000e-130 475


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3D01G280800 chr3D 388536927 388539647 2720 False 5025 5025 100.000 1 2721 1 chr3D.!!$F1 2720
1 TraesCS3D01G280800 chr3B 217383044 217385474 2430 True 3552 3552 93.130 305 2721 1 chr3B.!!$R2 2416
2 TraesCS3D01G280800 chr3B 217312191 217314513 2322 True 3336 3336 92.661 305 2620 1 chr3B.!!$R1 2315
3 TraesCS3D01G280800 chr3B 453196597 453197417 820 False 1072 1072 90.132 1891 2721 1 chr3B.!!$F2 830
4 TraesCS3D01G280800 chr3B 173224481 173225194 713 False 970 970 91.457 1953 2654 1 chr3B.!!$F1 701
5 TraesCS3D01G280800 chr5D 362178730 362181108 2378 True 3537 3537 93.543 310 2684 1 chr5D.!!$R1 2374
6 TraesCS3D01G280800 chr2D 315433792 315436209 2417 False 3472 3472 92.651 311 2720 1 chr2D.!!$F1 2409
7 TraesCS3D01G280800 chr7D 579951048 579953353 2305 False 3461 3461 93.774 310 2615 1 chr7D.!!$F2 2305
8 TraesCS3D01G280800 chr6D 380044446 380046853 2407 False 3454 3454 92.571 310 2721 1 chr6D.!!$F2 2411
9 TraesCS3D01G280800 chr5B 34272606 34275027 2421 True 3421 3421 92.257 310 2719 1 chr5B.!!$R1 2409
10 TraesCS3D01G280800 chr1D 407177451 407179859 2408 False 3373 3373 91.990 310 2717 1 chr1D.!!$F1 2407
11 TraesCS3D01G280800 chr1D 465921848 465924262 2414 True 3077 3077 89.715 311 2721 1 chr1D.!!$R1 2410
12 TraesCS3D01G280800 chr2B 730044798 730047217 2419 True 3317 3317 91.491 305 2712 1 chr2B.!!$R1 2407
13 TraesCS3D01G280800 chr1A 535099662 535101801 2139 True 3249 3249 94.112 311 2444 1 chr1A.!!$R1 2133
14 TraesCS3D01G280800 chr1A 259891493 259891993 500 False 416 416 81.980 2226 2721 1 chr1A.!!$F1 495
15 TraesCS3D01G280800 chr7B 685957510 685959927 2417 True 3022 3022 89.311 305 2712 1 chr7B.!!$R2 2407

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
177 178 0.038159 GATCACCGGGCTTCCTATCG 60.038 60.0 6.32 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 1964 1.264045 TGACCGCACCCTCATCATCA 61.264 55.0 0.0 0.0 0.0 3.07 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.465403 CAGGCAGGACTCCTCCCG 61.465 72.222 0.00 0.00 37.25 5.14
18 19 3.999285 AGGCAGGACTCCTCCCGT 61.999 66.667 0.00 0.00 37.25 5.28
19 20 3.775654 GGCAGGACTCCTCCCGTG 61.776 72.222 0.00 0.00 37.25 4.94
20 21 3.775654 GCAGGACTCCTCCCGTGG 61.776 72.222 0.00 0.00 37.25 4.94
21 22 2.037367 CAGGACTCCTCCCGTGGA 59.963 66.667 0.00 0.00 37.25 4.02
22 23 1.381872 CAGGACTCCTCCCGTGGAT 60.382 63.158 0.00 0.00 37.25 3.41
23 24 0.978146 CAGGACTCCTCCCGTGGATT 60.978 60.000 0.00 0.00 37.25 3.01
24 25 0.688087 AGGACTCCTCCCGTGGATTC 60.688 60.000 0.00 0.00 37.25 2.52
25 26 0.976073 GGACTCCTCCCGTGGATTCA 60.976 60.000 5.77 0.00 37.48 2.57
26 27 0.461961 GACTCCTCCCGTGGATTCAG 59.538 60.000 0.00 0.00 36.28 3.02
27 28 0.252284 ACTCCTCCCGTGGATTCAGT 60.252 55.000 0.00 0.00 35.30 3.41
28 29 0.905357 CTCCTCCCGTGGATTCAGTT 59.095 55.000 0.00 0.00 35.30 3.16
29 30 0.613260 TCCTCCCGTGGATTCAGTTG 59.387 55.000 0.00 0.00 0.00 3.16
30 31 0.392998 CCTCCCGTGGATTCAGTTGG 60.393 60.000 0.00 0.00 0.00 3.77
31 32 1.002624 TCCCGTGGATTCAGTTGGC 60.003 57.895 0.00 0.00 0.00 4.52
32 33 2.046285 CCCGTGGATTCAGTTGGCC 61.046 63.158 0.00 0.00 0.00 5.36
33 34 1.303236 CCGTGGATTCAGTTGGCCA 60.303 57.895 0.00 0.00 0.00 5.36
34 35 1.308069 CCGTGGATTCAGTTGGCCAG 61.308 60.000 5.11 0.00 0.00 4.85
35 36 1.885871 GTGGATTCAGTTGGCCAGC 59.114 57.895 12.39 12.39 0.00 4.85
36 37 1.304381 TGGATTCAGTTGGCCAGCC 60.304 57.895 16.95 6.15 0.00 4.85
37 38 2.054453 GGATTCAGTTGGCCAGCCC 61.054 63.158 16.95 6.00 34.56 5.19
38 39 2.361610 ATTCAGTTGGCCAGCCCG 60.362 61.111 16.95 8.16 35.87 6.13
39 40 3.210012 ATTCAGTTGGCCAGCCCGT 62.210 57.895 16.95 0.00 35.87 5.28
40 41 3.842925 TTCAGTTGGCCAGCCCGTC 62.843 63.158 16.95 0.00 35.87 4.79
54 55 4.351938 CGTCCACGCCGAACCTCA 62.352 66.667 0.00 0.00 0.00 3.86
55 56 2.029964 GTCCACGCCGAACCTCAA 59.970 61.111 0.00 0.00 0.00 3.02
56 57 2.029964 TCCACGCCGAACCTCAAC 59.970 61.111 0.00 0.00 0.00 3.18
57 58 3.411351 CCACGCCGAACCTCAACG 61.411 66.667 0.00 0.00 0.00 4.10
58 59 4.072088 CACGCCGAACCTCAACGC 62.072 66.667 0.00 0.00 0.00 4.84
59 60 4.295119 ACGCCGAACCTCAACGCT 62.295 61.111 0.00 0.00 0.00 5.07
60 61 3.479269 CGCCGAACCTCAACGCTC 61.479 66.667 0.00 0.00 0.00 5.03
61 62 3.119096 GCCGAACCTCAACGCTCC 61.119 66.667 0.00 0.00 0.00 4.70
62 63 2.342279 CCGAACCTCAACGCTCCA 59.658 61.111 0.00 0.00 0.00 3.86
63 64 2.027625 CCGAACCTCAACGCTCCAC 61.028 63.158 0.00 0.00 0.00 4.02
64 65 1.006102 CGAACCTCAACGCTCCACT 60.006 57.895 0.00 0.00 0.00 4.00
65 66 1.284982 CGAACCTCAACGCTCCACTG 61.285 60.000 0.00 0.00 0.00 3.66
66 67 0.951040 GAACCTCAACGCTCCACTGG 60.951 60.000 0.00 0.00 0.00 4.00
67 68 1.696097 AACCTCAACGCTCCACTGGT 61.696 55.000 0.00 0.00 0.00 4.00
68 69 1.669115 CCTCAACGCTCCACTGGTG 60.669 63.158 0.00 0.00 0.00 4.17
69 70 1.367471 CTCAACGCTCCACTGGTGA 59.633 57.895 1.93 0.00 0.00 4.02
70 71 0.946221 CTCAACGCTCCACTGGTGAC 60.946 60.000 1.93 0.00 0.00 3.67
71 72 1.961277 CAACGCTCCACTGGTGACC 60.961 63.158 0.00 0.00 0.00 4.02
72 73 2.140792 AACGCTCCACTGGTGACCT 61.141 57.895 2.11 0.00 0.00 3.85
73 74 2.100879 AACGCTCCACTGGTGACCTC 62.101 60.000 2.11 0.00 0.00 3.85
74 75 2.279069 CGCTCCACTGGTGACCTCT 61.279 63.158 2.11 0.00 0.00 3.69
75 76 1.594310 GCTCCACTGGTGACCTCTC 59.406 63.158 2.11 0.00 0.00 3.20
76 77 0.902516 GCTCCACTGGTGACCTCTCT 60.903 60.000 2.11 0.00 0.00 3.10
77 78 1.638529 CTCCACTGGTGACCTCTCTT 58.361 55.000 2.11 0.00 0.00 2.85
78 79 1.274728 CTCCACTGGTGACCTCTCTTG 59.725 57.143 2.11 0.00 0.00 3.02
79 80 0.321122 CCACTGGTGACCTCTCTTGC 60.321 60.000 2.11 0.00 0.00 4.01
80 81 0.683973 CACTGGTGACCTCTCTTGCT 59.316 55.000 2.11 0.00 0.00 3.91
81 82 0.683973 ACTGGTGACCTCTCTTGCTG 59.316 55.000 2.11 0.00 0.00 4.41
82 83 0.972134 CTGGTGACCTCTCTTGCTGA 59.028 55.000 2.11 0.00 0.00 4.26
83 84 1.554160 CTGGTGACCTCTCTTGCTGAT 59.446 52.381 2.11 0.00 0.00 2.90
84 85 1.552337 TGGTGACCTCTCTTGCTGATC 59.448 52.381 2.11 0.00 0.00 2.92
85 86 1.470632 GGTGACCTCTCTTGCTGATCG 60.471 57.143 0.00 0.00 0.00 3.69
86 87 0.820226 TGACCTCTCTTGCTGATCGG 59.180 55.000 0.00 0.00 0.00 4.18
87 88 0.820871 GACCTCTCTTGCTGATCGGT 59.179 55.000 2.89 0.00 32.21 4.69
88 89 0.534412 ACCTCTCTTGCTGATCGGTG 59.466 55.000 2.89 0.00 0.00 4.94
89 90 0.179089 CCTCTCTTGCTGATCGGTGG 60.179 60.000 2.89 0.00 0.00 4.61
90 91 0.820226 CTCTCTTGCTGATCGGTGGA 59.180 55.000 2.89 0.00 0.00 4.02
91 92 0.820226 TCTCTTGCTGATCGGTGGAG 59.180 55.000 2.89 8.46 0.00 3.86
92 93 0.179089 CTCTTGCTGATCGGTGGAGG 60.179 60.000 2.89 0.00 0.00 4.30
93 94 1.817099 CTTGCTGATCGGTGGAGGC 60.817 63.158 2.89 0.00 0.00 4.70
94 95 3.329542 TTGCTGATCGGTGGAGGCC 62.330 63.158 2.89 0.00 0.00 5.19
115 116 2.086054 GAGACGCACAGTTTCCATCT 57.914 50.000 0.00 0.00 0.00 2.90
116 117 2.417719 GAGACGCACAGTTTCCATCTT 58.582 47.619 0.00 0.00 0.00 2.40
117 118 2.808543 GAGACGCACAGTTTCCATCTTT 59.191 45.455 0.00 0.00 0.00 2.52
118 119 2.549754 AGACGCACAGTTTCCATCTTTG 59.450 45.455 0.00 0.00 0.00 2.77
119 120 1.608590 ACGCACAGTTTCCATCTTTGG 59.391 47.619 0.00 0.00 45.15 3.28
128 129 3.890527 CCATCTTTGGACTGGGGAG 57.109 57.895 0.00 0.00 46.92 4.30
129 130 1.289160 CCATCTTTGGACTGGGGAGA 58.711 55.000 0.00 0.00 46.92 3.71
130 131 1.849039 CCATCTTTGGACTGGGGAGAT 59.151 52.381 0.00 0.00 46.92 2.75
131 132 2.422519 CCATCTTTGGACTGGGGAGATG 60.423 54.545 5.01 5.01 46.92 2.90
132 133 2.342406 TCTTTGGACTGGGGAGATGA 57.658 50.000 0.00 0.00 0.00 2.92
133 134 1.909302 TCTTTGGACTGGGGAGATGAC 59.091 52.381 0.00 0.00 0.00 3.06
134 135 0.991920 TTTGGACTGGGGAGATGACC 59.008 55.000 0.00 0.00 0.00 4.02
135 136 1.264749 TTGGACTGGGGAGATGACCG 61.265 60.000 0.00 0.00 0.00 4.79
136 137 2.501610 GACTGGGGAGATGACCGC 59.498 66.667 0.00 0.00 42.15 5.68
137 138 3.432051 GACTGGGGAGATGACCGCG 62.432 68.421 0.00 0.00 44.26 6.46
138 139 3.147595 CTGGGGAGATGACCGCGA 61.148 66.667 8.23 0.00 44.26 5.87
139 140 3.432051 CTGGGGAGATGACCGCGAC 62.432 68.421 8.23 1.20 44.26 5.19
140 141 4.570663 GGGGAGATGACCGCGACG 62.571 72.222 8.23 0.00 33.50 5.12
142 143 4.194720 GGAGATGACCGCGACGCT 62.195 66.667 19.02 0.00 0.00 5.07
143 144 2.652496 GAGATGACCGCGACGCTC 60.652 66.667 19.02 10.22 0.00 5.03
144 145 4.538283 AGATGACCGCGACGCTCG 62.538 66.667 19.02 10.20 43.89 5.03
145 146 4.531912 GATGACCGCGACGCTCGA 62.532 66.667 19.02 0.00 43.74 4.04
146 147 4.538283 ATGACCGCGACGCTCGAG 62.538 66.667 19.02 8.45 43.74 4.04
157 158 4.537433 GCTCGAGGATGCCGCCTT 62.537 66.667 15.58 0.00 38.73 4.35
158 159 2.587194 CTCGAGGATGCCGCCTTG 60.587 66.667 3.91 3.34 38.73 3.61
159 160 3.074369 TCGAGGATGCCGCCTTGA 61.074 61.111 7.60 7.60 44.43 3.02
160 161 2.109799 CGAGGATGCCGCCTTGAT 59.890 61.111 3.62 0.00 41.25 2.57
161 162 1.958205 CGAGGATGCCGCCTTGATC 60.958 63.158 3.62 0.00 41.25 2.92
162 163 1.146930 GAGGATGCCGCCTTGATCA 59.853 57.895 0.00 0.00 38.73 2.92
163 164 1.153086 AGGATGCCGCCTTGATCAC 60.153 57.895 0.00 0.00 33.46 3.06
164 165 2.189499 GGATGCCGCCTTGATCACC 61.189 63.158 0.00 0.00 0.00 4.02
165 166 2.514592 ATGCCGCCTTGATCACCG 60.515 61.111 0.00 0.00 0.00 4.94
166 167 4.776322 TGCCGCCTTGATCACCGG 62.776 66.667 19.12 19.12 43.38 5.28
169 170 4.473520 CGCCTTGATCACCGGGCT 62.474 66.667 22.80 0.00 42.13 5.19
170 171 2.044946 GCCTTGATCACCGGGCTT 60.045 61.111 20.04 0.00 41.20 4.35
171 172 2.115291 GCCTTGATCACCGGGCTTC 61.115 63.158 20.04 0.00 41.20 3.86
172 173 1.452108 CCTTGATCACCGGGCTTCC 60.452 63.158 6.32 0.00 0.00 3.46
173 174 1.604378 CTTGATCACCGGGCTTCCT 59.396 57.895 6.32 0.00 0.00 3.36
174 175 0.830648 CTTGATCACCGGGCTTCCTA 59.169 55.000 6.32 0.00 0.00 2.94
175 176 1.417890 CTTGATCACCGGGCTTCCTAT 59.582 52.381 6.32 0.00 0.00 2.57
176 177 1.048601 TGATCACCGGGCTTCCTATC 58.951 55.000 6.32 0.00 0.00 2.08
177 178 0.038159 GATCACCGGGCTTCCTATCG 60.038 60.000 6.32 0.00 0.00 2.92
178 179 0.469331 ATCACCGGGCTTCCTATCGA 60.469 55.000 6.32 0.00 0.00 3.59
179 180 1.067582 CACCGGGCTTCCTATCGAC 59.932 63.158 6.32 0.00 0.00 4.20
180 181 2.335369 CCGGGCTTCCTATCGACG 59.665 66.667 0.00 0.00 0.00 5.12
181 182 2.335369 CGGGCTTCCTATCGACGG 59.665 66.667 0.00 0.00 0.00 4.79
182 183 2.735237 GGGCTTCCTATCGACGGG 59.265 66.667 0.00 1.28 0.00 5.28
183 184 1.831286 GGGCTTCCTATCGACGGGA 60.831 63.158 4.31 4.31 0.00 5.14
184 185 1.660917 GGCTTCCTATCGACGGGAG 59.339 63.158 6.53 6.53 32.80 4.30
185 186 1.660917 GCTTCCTATCGACGGGAGG 59.339 63.158 11.75 11.66 32.80 4.30
186 187 1.660917 CTTCCTATCGACGGGAGGC 59.339 63.158 10.19 0.00 32.80 4.70
187 188 1.807495 CTTCCTATCGACGGGAGGCC 61.807 65.000 10.19 0.00 32.80 5.19
188 189 2.520982 CCTATCGACGGGAGGCCA 60.521 66.667 5.01 0.00 0.00 5.36
189 190 2.728817 CTATCGACGGGAGGCCAC 59.271 66.667 5.01 0.00 0.00 5.01
190 191 1.828660 CTATCGACGGGAGGCCACT 60.829 63.158 5.01 0.00 0.00 4.00
191 192 0.536687 CTATCGACGGGAGGCCACTA 60.537 60.000 5.01 0.00 0.00 2.74
192 193 0.111832 TATCGACGGGAGGCCACTAT 59.888 55.000 5.01 0.00 0.00 2.12
193 194 1.464376 ATCGACGGGAGGCCACTATG 61.464 60.000 5.01 0.00 0.00 2.23
194 195 2.423898 CGACGGGAGGCCACTATGT 61.424 63.158 5.01 0.00 0.00 2.29
195 196 1.105167 CGACGGGAGGCCACTATGTA 61.105 60.000 5.01 0.00 0.00 2.29
196 197 1.339097 GACGGGAGGCCACTATGTAT 58.661 55.000 5.01 0.00 0.00 2.29
197 198 1.000955 GACGGGAGGCCACTATGTATG 59.999 57.143 5.01 0.00 0.00 2.39
198 199 1.338107 CGGGAGGCCACTATGTATGA 58.662 55.000 5.01 0.00 0.00 2.15
199 200 1.273606 CGGGAGGCCACTATGTATGAG 59.726 57.143 5.01 0.00 0.00 2.90
200 201 1.002544 GGGAGGCCACTATGTATGAGC 59.997 57.143 5.01 0.00 0.00 4.26
201 202 1.694150 GGAGGCCACTATGTATGAGCA 59.306 52.381 5.01 0.00 0.00 4.26
202 203 2.548920 GGAGGCCACTATGTATGAGCAC 60.549 54.545 5.01 0.00 0.00 4.40
203 204 1.417890 AGGCCACTATGTATGAGCACC 59.582 52.381 5.01 0.00 0.00 5.01
204 205 1.502231 GCCACTATGTATGAGCACCG 58.498 55.000 0.00 0.00 0.00 4.94
205 206 1.068588 GCCACTATGTATGAGCACCGA 59.931 52.381 0.00 0.00 0.00 4.69
206 207 2.289072 GCCACTATGTATGAGCACCGAT 60.289 50.000 0.00 0.00 0.00 4.18
207 208 3.803715 GCCACTATGTATGAGCACCGATT 60.804 47.826 0.00 0.00 0.00 3.34
208 209 3.990469 CCACTATGTATGAGCACCGATTC 59.010 47.826 0.00 0.00 0.00 2.52
209 210 3.990469 CACTATGTATGAGCACCGATTCC 59.010 47.826 0.00 0.00 0.00 3.01
210 211 2.154854 ATGTATGAGCACCGATTCCG 57.845 50.000 0.00 0.00 0.00 4.30
211 212 1.107945 TGTATGAGCACCGATTCCGA 58.892 50.000 0.00 0.00 38.22 4.55
212 213 1.686587 TGTATGAGCACCGATTCCGAT 59.313 47.619 0.00 0.00 38.22 4.18
213 214 2.061773 GTATGAGCACCGATTCCGATG 58.938 52.381 0.00 0.00 38.22 3.84
214 215 0.250038 ATGAGCACCGATTCCGATGG 60.250 55.000 0.00 0.00 38.22 3.51
215 216 1.595382 GAGCACCGATTCCGATGGG 60.595 63.158 0.00 0.00 38.22 4.00
216 217 2.189521 GCACCGATTCCGATGGGT 59.810 61.111 0.00 0.00 44.23 4.51
218 219 2.908015 ACCGATTCCGATGGGTGG 59.092 61.111 0.00 0.00 42.11 4.61
219 220 2.591715 CCGATTCCGATGGGTGGC 60.592 66.667 0.00 0.00 38.22 5.01
220 221 2.967076 CGATTCCGATGGGTGGCG 60.967 66.667 0.00 0.00 38.22 5.69
221 222 3.279875 GATTCCGATGGGTGGCGC 61.280 66.667 0.00 0.00 33.83 6.53
247 248 6.814506 GCAGATGATTGCTCTTATTGGTAT 57.185 37.500 0.00 0.00 40.89 2.73
248 249 6.609533 GCAGATGATTGCTCTTATTGGTATG 58.390 40.000 0.00 0.00 40.89 2.39
249 250 6.349115 GCAGATGATTGCTCTTATTGGTATGG 60.349 42.308 0.00 0.00 40.89 2.74
250 251 5.709164 AGATGATTGCTCTTATTGGTATGGC 59.291 40.000 0.00 0.00 0.00 4.40
251 252 5.052693 TGATTGCTCTTATTGGTATGGCT 57.947 39.130 0.00 0.00 0.00 4.75
252 253 5.065914 TGATTGCTCTTATTGGTATGGCTC 58.934 41.667 0.00 0.00 0.00 4.70
253 254 3.492102 TGCTCTTATTGGTATGGCTCC 57.508 47.619 0.00 0.00 0.00 4.70
254 255 3.048600 TGCTCTTATTGGTATGGCTCCT 58.951 45.455 0.00 0.00 0.00 3.69
255 256 4.231273 TGCTCTTATTGGTATGGCTCCTA 58.769 43.478 0.00 0.00 0.00 2.94
256 257 4.040461 TGCTCTTATTGGTATGGCTCCTAC 59.960 45.833 0.00 0.00 0.00 3.18
257 258 4.563786 GCTCTTATTGGTATGGCTCCTACC 60.564 50.000 5.02 5.02 39.31 3.18
258 259 3.576982 TCTTATTGGTATGGCTCCTACCG 59.423 47.826 6.89 0.00 41.35 4.02
259 260 2.097110 ATTGGTATGGCTCCTACCGA 57.903 50.000 4.58 4.58 41.35 4.69
260 261 1.410004 TTGGTATGGCTCCTACCGAG 58.590 55.000 6.89 0.00 41.35 4.63
261 262 0.469331 TGGTATGGCTCCTACCGAGG 60.469 60.000 6.89 0.00 45.35 4.63
267 268 2.042800 GCTCCTACCGAGGCTAAGG 58.957 63.158 6.92 6.92 43.40 2.69
268 269 0.756070 GCTCCTACCGAGGCTAAGGT 60.756 60.000 16.82 16.82 43.40 3.50
269 270 1.777941 CTCCTACCGAGGCTAAGGTT 58.222 55.000 17.66 4.65 43.40 3.50
270 271 1.409427 CTCCTACCGAGGCTAAGGTTG 59.591 57.143 17.66 15.33 43.40 3.77
271 272 1.006281 TCCTACCGAGGCTAAGGTTGA 59.994 52.381 17.66 12.46 43.40 3.18
272 273 2.040178 CCTACCGAGGCTAAGGTTGAT 58.960 52.381 17.66 0.00 41.63 2.57
273 274 2.224066 CCTACCGAGGCTAAGGTTGATG 60.224 54.545 17.66 7.65 41.63 3.07
274 275 1.276622 ACCGAGGCTAAGGTTGATGT 58.723 50.000 8.19 0.00 37.49 3.06
275 276 2.463752 ACCGAGGCTAAGGTTGATGTA 58.536 47.619 8.19 0.00 37.49 2.29
276 277 2.431057 ACCGAGGCTAAGGTTGATGTAG 59.569 50.000 8.19 0.00 37.49 2.74
277 278 2.693591 CCGAGGCTAAGGTTGATGTAGA 59.306 50.000 0.00 0.00 0.00 2.59
278 279 3.243569 CCGAGGCTAAGGTTGATGTAGAG 60.244 52.174 0.00 0.00 0.00 2.43
279 280 3.243569 CGAGGCTAAGGTTGATGTAGAGG 60.244 52.174 0.00 0.00 0.00 3.69
280 281 3.961408 GAGGCTAAGGTTGATGTAGAGGA 59.039 47.826 0.00 0.00 0.00 3.71
281 282 3.964031 AGGCTAAGGTTGATGTAGAGGAG 59.036 47.826 0.00 0.00 0.00 3.69
282 283 3.070302 GGCTAAGGTTGATGTAGAGGAGG 59.930 52.174 0.00 0.00 0.00 4.30
283 284 3.070302 GCTAAGGTTGATGTAGAGGAGGG 59.930 52.174 0.00 0.00 0.00 4.30
284 285 3.491766 AAGGTTGATGTAGAGGAGGGA 57.508 47.619 0.00 0.00 0.00 4.20
285 286 3.039252 AGGTTGATGTAGAGGAGGGAG 57.961 52.381 0.00 0.00 0.00 4.30
286 287 2.587777 AGGTTGATGTAGAGGAGGGAGA 59.412 50.000 0.00 0.00 0.00 3.71
287 288 3.012959 AGGTTGATGTAGAGGAGGGAGAA 59.987 47.826 0.00 0.00 0.00 2.87
288 289 3.386402 GGTTGATGTAGAGGAGGGAGAAG 59.614 52.174 0.00 0.00 0.00 2.85
289 290 4.282496 GTTGATGTAGAGGAGGGAGAAGA 58.718 47.826 0.00 0.00 0.00 2.87
290 291 4.177537 TGATGTAGAGGAGGGAGAAGAG 57.822 50.000 0.00 0.00 0.00 2.85
291 292 2.445682 TGTAGAGGAGGGAGAAGAGC 57.554 55.000 0.00 0.00 0.00 4.09
292 293 1.641192 TGTAGAGGAGGGAGAAGAGCA 59.359 52.381 0.00 0.00 0.00 4.26
293 294 2.306847 GTAGAGGAGGGAGAAGAGCAG 58.693 57.143 0.00 0.00 0.00 4.24
294 295 1.006813 AGAGGAGGGAGAAGAGCAGA 58.993 55.000 0.00 0.00 0.00 4.26
295 296 1.360852 AGAGGAGGGAGAAGAGCAGAA 59.639 52.381 0.00 0.00 0.00 3.02
296 297 1.756538 GAGGAGGGAGAAGAGCAGAAG 59.243 57.143 0.00 0.00 0.00 2.85
297 298 1.360852 AGGAGGGAGAAGAGCAGAAGA 59.639 52.381 0.00 0.00 0.00 2.87
298 299 2.183679 GGAGGGAGAAGAGCAGAAGAA 58.816 52.381 0.00 0.00 0.00 2.52
299 300 2.168313 GGAGGGAGAAGAGCAGAAGAAG 59.832 54.545 0.00 0.00 0.00 2.85
300 301 3.096092 GAGGGAGAAGAGCAGAAGAAGA 58.904 50.000 0.00 0.00 0.00 2.87
301 302 3.513515 GAGGGAGAAGAGCAGAAGAAGAA 59.486 47.826 0.00 0.00 0.00 2.52
302 303 3.515104 AGGGAGAAGAGCAGAAGAAGAAG 59.485 47.826 0.00 0.00 0.00 2.85
303 304 3.369366 GGGAGAAGAGCAGAAGAAGAAGG 60.369 52.174 0.00 0.00 0.00 3.46
404 407 2.224209 TGTCTCGAGGACTTTGTTTCCC 60.224 50.000 13.56 0.00 44.74 3.97
452 455 1.598130 GTGGCTGAAGGCGTTGACT 60.598 57.895 0.00 0.00 44.42 3.41
545 548 7.077605 TGTTTTGCTATCAAGTCATTTCTTCG 58.922 34.615 0.00 0.00 33.12 3.79
1083 1086 2.884012 TGAGTTTCATTTGCCACATCGT 59.116 40.909 0.00 0.00 0.00 3.73
1104 1107 3.866910 GTGTGTTTCGTCAGTTTGGTCTA 59.133 43.478 0.00 0.00 0.00 2.59
1161 1164 6.820656 CAGACAAAGCACTTCATAGGTAAGAT 59.179 38.462 0.00 0.00 0.00 2.40
1192 1195 3.059884 CGTATTGACTAAGCATCGCCAT 58.940 45.455 0.00 0.00 0.00 4.40
1300 1303 0.320374 ATGCATCGTATGGTACCCGG 59.680 55.000 10.07 0.00 0.00 5.73
1304 1307 1.409790 CATCGTATGGTACCCGGTTCA 59.590 52.381 10.07 0.00 0.00 3.18
1332 1335 1.202592 TGTGGAGCAAGCTCGTAACAA 60.203 47.619 15.20 3.63 43.59 2.83
1404 1407 7.360113 ACCTACAATGGTTTCTTGAAAATGT 57.640 32.000 0.00 4.51 36.89 2.71
1456 1459 5.543507 ACGATGATATTCTTGAAGAGCCT 57.456 39.130 0.00 0.00 0.00 4.58
1779 1785 7.826744 TCCATGTTACATATGTTGCAGAGTTTA 59.173 33.333 14.77 0.00 0.00 2.01
1896 1902 2.738587 TCTGCCTCTAGGTCTGGTAG 57.261 55.000 0.00 0.00 37.57 3.18
1898 1904 2.786445 TCTGCCTCTAGGTCTGGTAGAT 59.214 50.000 0.00 0.00 37.60 1.98
1957 1964 7.129457 TGTGAGTTCCTCATATGCTTATCTT 57.871 36.000 0.00 0.00 42.73 2.40
2000 2007 5.859495 CCCAAGAGGTATGACTAATCCTTC 58.141 45.833 0.00 0.00 0.00 3.46
2105 2112 2.668212 TTTGGCGGACGCTCAAGG 60.668 61.111 16.72 0.00 41.60 3.61
2290 2300 3.940221 CAGGAAGAAGAAGATTGCCTCTG 59.060 47.826 0.00 0.00 33.29 3.35
2461 2487 9.216117 ACTTGTAGTAATGTTGAATTGTCCTAC 57.784 33.333 0.00 0.00 0.00 3.18
2529 2560 6.823182 TGCAGTTTACAGCACTACATTCATAT 59.177 34.615 0.00 0.00 33.35 1.78
2553 2592 1.677576 TGAGTTCAGTTTGCAGCCAAG 59.322 47.619 0.00 0.00 31.52 3.61
2622 2662 1.669115 ACTAAGGCGCTGCACTGTG 60.669 57.895 7.64 2.76 0.00 3.66
2627 2667 3.043713 GCGCTGCACTGTGCTGTA 61.044 61.111 31.15 14.62 45.31 2.74
2690 2730 4.845580 CCCCTAGGCGCTGCACAG 62.846 72.222 7.64 0.00 0.00 3.66
2713 2755 1.906253 CTGTGCATCCAGAGAGCCT 59.094 57.895 0.00 0.00 34.44 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.688087 GAATCCACGGGAGGAGTCCT 60.688 60.000 12.85 12.85 44.74 3.85
6 7 1.823976 GAATCCACGGGAGGAGTCC 59.176 63.158 0.00 0.00 44.74 3.85
8 9 0.252284 ACTGAATCCACGGGAGGAGT 60.252 55.000 0.00 0.00 41.90 3.85
9 10 0.905357 AACTGAATCCACGGGAGGAG 59.095 55.000 0.00 0.00 41.90 3.69
10 11 0.613260 CAACTGAATCCACGGGAGGA 59.387 55.000 0.00 0.00 43.01 3.71
11 12 0.392998 CCAACTGAATCCACGGGAGG 60.393 60.000 0.00 0.00 34.05 4.30
12 13 1.026718 GCCAACTGAATCCACGGGAG 61.027 60.000 0.00 0.00 34.05 4.30
13 14 1.002624 GCCAACTGAATCCACGGGA 60.003 57.895 0.00 0.00 35.55 5.14
14 15 2.046285 GGCCAACTGAATCCACGGG 61.046 63.158 0.00 0.00 0.00 5.28
15 16 1.303236 TGGCCAACTGAATCCACGG 60.303 57.895 0.61 0.00 0.00 4.94
16 17 1.926511 GCTGGCCAACTGAATCCACG 61.927 60.000 7.01 0.00 0.00 4.94
17 18 1.598701 GGCTGGCCAACTGAATCCAC 61.599 60.000 7.01 0.00 35.81 4.02
18 19 1.304381 GGCTGGCCAACTGAATCCA 60.304 57.895 7.01 0.00 35.81 3.41
19 20 2.054453 GGGCTGGCCAACTGAATCC 61.054 63.158 16.34 0.00 37.98 3.01
20 21 2.409870 CGGGCTGGCCAACTGAATC 61.410 63.158 21.03 0.00 37.98 2.52
21 22 2.361610 CGGGCTGGCCAACTGAAT 60.362 61.111 21.03 0.00 37.98 2.57
22 23 3.842925 GACGGGCTGGCCAACTGAA 62.843 63.158 21.03 0.00 37.98 3.02
23 24 4.329545 GACGGGCTGGCCAACTGA 62.330 66.667 21.03 0.00 37.98 3.41
37 38 3.851845 TTGAGGTTCGGCGTGGACG 62.852 63.158 6.85 0.00 43.27 4.79
38 39 2.029964 TTGAGGTTCGGCGTGGAC 59.970 61.111 6.85 4.50 0.00 4.02
39 40 2.029964 GTTGAGGTTCGGCGTGGA 59.970 61.111 6.85 0.00 0.00 4.02
40 41 3.411351 CGTTGAGGTTCGGCGTGG 61.411 66.667 6.85 0.00 0.00 4.94
41 42 4.072088 GCGTTGAGGTTCGGCGTG 62.072 66.667 6.85 0.00 0.00 5.34
42 43 4.295119 AGCGTTGAGGTTCGGCGT 62.295 61.111 6.85 0.00 0.00 5.68
43 44 3.479269 GAGCGTTGAGGTTCGGCG 61.479 66.667 0.00 0.00 0.00 6.46
44 45 3.119096 GGAGCGTTGAGGTTCGGC 61.119 66.667 0.00 0.00 0.00 5.54
45 46 2.027625 GTGGAGCGTTGAGGTTCGG 61.028 63.158 0.00 0.00 0.00 4.30
46 47 1.006102 AGTGGAGCGTTGAGGTTCG 60.006 57.895 0.00 0.00 0.00 3.95
47 48 0.951040 CCAGTGGAGCGTTGAGGTTC 60.951 60.000 1.68 0.00 0.00 3.62
48 49 1.071471 CCAGTGGAGCGTTGAGGTT 59.929 57.895 1.68 0.00 0.00 3.50
49 50 2.140792 ACCAGTGGAGCGTTGAGGT 61.141 57.895 18.40 0.00 0.00 3.85
50 51 1.669115 CACCAGTGGAGCGTTGAGG 60.669 63.158 18.40 0.00 0.00 3.86
51 52 0.946221 GTCACCAGTGGAGCGTTGAG 60.946 60.000 18.40 0.00 0.00 3.02
52 53 1.069090 GTCACCAGTGGAGCGTTGA 59.931 57.895 18.40 5.66 0.00 3.18
53 54 1.961277 GGTCACCAGTGGAGCGTTG 60.961 63.158 18.40 2.85 0.00 4.10
54 55 2.100879 GAGGTCACCAGTGGAGCGTT 62.101 60.000 18.40 0.00 37.81 4.84
55 56 2.524394 AGGTCACCAGTGGAGCGT 60.524 61.111 18.40 3.37 37.81 5.07
56 57 2.219325 GAGAGGTCACCAGTGGAGCG 62.219 65.000 18.40 3.77 37.81 5.03
57 58 0.902516 AGAGAGGTCACCAGTGGAGC 60.903 60.000 18.40 3.74 0.00 4.70
58 59 1.274728 CAAGAGAGGTCACCAGTGGAG 59.725 57.143 18.40 8.55 0.00 3.86
59 60 1.342074 CAAGAGAGGTCACCAGTGGA 58.658 55.000 18.40 0.00 0.00 4.02
60 61 0.321122 GCAAGAGAGGTCACCAGTGG 60.321 60.000 7.91 7.91 0.00 4.00
61 62 0.683973 AGCAAGAGAGGTCACCAGTG 59.316 55.000 0.00 0.00 0.00 3.66
62 63 0.683973 CAGCAAGAGAGGTCACCAGT 59.316 55.000 0.00 0.00 0.00 4.00
63 64 0.972134 TCAGCAAGAGAGGTCACCAG 59.028 55.000 0.00 0.00 0.00 4.00
64 65 1.552337 GATCAGCAAGAGAGGTCACCA 59.448 52.381 0.00 0.00 0.00 4.17
65 66 1.470632 CGATCAGCAAGAGAGGTCACC 60.471 57.143 0.00 0.00 0.00 4.02
66 67 1.470632 CCGATCAGCAAGAGAGGTCAC 60.471 57.143 0.00 0.00 0.00 3.67
67 68 0.820226 CCGATCAGCAAGAGAGGTCA 59.180 55.000 0.00 0.00 0.00 4.02
68 69 0.820871 ACCGATCAGCAAGAGAGGTC 59.179 55.000 0.00 0.00 35.77 3.85
69 70 0.534412 CACCGATCAGCAAGAGAGGT 59.466 55.000 0.00 0.00 39.58 3.85
70 71 0.179089 CCACCGATCAGCAAGAGAGG 60.179 60.000 0.00 0.00 34.15 3.69
71 72 0.820226 TCCACCGATCAGCAAGAGAG 59.180 55.000 0.00 0.00 0.00 3.20
72 73 0.820226 CTCCACCGATCAGCAAGAGA 59.180 55.000 0.00 0.00 0.00 3.10
73 74 0.179089 CCTCCACCGATCAGCAAGAG 60.179 60.000 0.00 0.00 0.00 2.85
74 75 1.900351 CCTCCACCGATCAGCAAGA 59.100 57.895 0.00 0.00 0.00 3.02
75 76 1.817099 GCCTCCACCGATCAGCAAG 60.817 63.158 0.00 0.00 0.00 4.01
76 77 2.268920 GCCTCCACCGATCAGCAA 59.731 61.111 0.00 0.00 0.00 3.91
77 78 3.785859 GGCCTCCACCGATCAGCA 61.786 66.667 0.00 0.00 0.00 4.41
89 90 4.803426 CTGTGCGTCTCCGGCCTC 62.803 72.222 0.00 0.00 33.68 4.70
91 92 4.681978 AACTGTGCGTCTCCGGCC 62.682 66.667 0.00 0.00 33.68 6.13
92 93 2.665185 AAACTGTGCGTCTCCGGC 60.665 61.111 0.00 0.00 33.68 6.13
93 94 2.027625 GGAAACTGTGCGTCTCCGG 61.028 63.158 0.00 0.00 33.68 5.14
94 95 0.670546 ATGGAAACTGTGCGTCTCCG 60.671 55.000 0.00 0.00 37.07 4.63
95 96 1.079503 GATGGAAACTGTGCGTCTCC 58.920 55.000 0.00 0.00 31.12 3.71
96 97 2.086054 AGATGGAAACTGTGCGTCTC 57.914 50.000 0.00 0.00 39.60 3.36
97 98 2.549754 CAAAGATGGAAACTGTGCGTCT 59.450 45.455 0.00 0.00 45.22 4.18
98 99 2.921126 CAAAGATGGAAACTGTGCGTC 58.079 47.619 0.00 0.00 33.89 5.19
111 112 2.507058 TCATCTCCCCAGTCCAAAGATG 59.493 50.000 4.65 4.65 42.93 2.90
112 113 2.507471 GTCATCTCCCCAGTCCAAAGAT 59.493 50.000 0.00 0.00 0.00 2.40
113 114 1.909302 GTCATCTCCCCAGTCCAAAGA 59.091 52.381 0.00 0.00 0.00 2.52
114 115 1.065126 GGTCATCTCCCCAGTCCAAAG 60.065 57.143 0.00 0.00 0.00 2.77
115 116 0.991920 GGTCATCTCCCCAGTCCAAA 59.008 55.000 0.00 0.00 0.00 3.28
116 117 1.264749 CGGTCATCTCCCCAGTCCAA 61.265 60.000 0.00 0.00 0.00 3.53
117 118 1.685765 CGGTCATCTCCCCAGTCCA 60.686 63.158 0.00 0.00 0.00 4.02
118 119 3.095347 GCGGTCATCTCCCCAGTCC 62.095 68.421 0.00 0.00 0.00 3.85
119 120 2.501610 GCGGTCATCTCCCCAGTC 59.498 66.667 0.00 0.00 0.00 3.51
120 121 3.461773 CGCGGTCATCTCCCCAGT 61.462 66.667 0.00 0.00 0.00 4.00
121 122 3.147595 TCGCGGTCATCTCCCCAG 61.148 66.667 6.13 0.00 0.00 4.45
122 123 3.458163 GTCGCGGTCATCTCCCCA 61.458 66.667 6.13 0.00 0.00 4.96
123 124 4.570663 CGTCGCGGTCATCTCCCC 62.571 72.222 6.13 0.00 0.00 4.81
125 126 4.194720 AGCGTCGCGGTCATCTCC 62.195 66.667 12.30 0.00 29.31 3.71
140 141 4.537433 AAGGCGGCATCCTCGAGC 62.537 66.667 13.08 0.00 34.82 5.03
141 142 2.374830 ATCAAGGCGGCATCCTCGAG 62.375 60.000 13.08 5.13 34.82 4.04
142 143 2.369257 GATCAAGGCGGCATCCTCGA 62.369 60.000 13.08 0.00 34.82 4.04
143 144 1.958205 GATCAAGGCGGCATCCTCG 60.958 63.158 13.08 0.00 34.82 4.63
144 145 1.146930 TGATCAAGGCGGCATCCTC 59.853 57.895 13.08 3.13 34.82 3.71
145 146 1.153086 GTGATCAAGGCGGCATCCT 60.153 57.895 13.08 0.00 38.31 3.24
146 147 2.189499 GGTGATCAAGGCGGCATCC 61.189 63.158 13.08 0.00 0.00 3.51
147 148 2.537560 CGGTGATCAAGGCGGCATC 61.538 63.158 13.08 6.27 0.00 3.91
148 149 2.514592 CGGTGATCAAGGCGGCAT 60.515 61.111 13.08 0.00 0.00 4.40
149 150 4.776322 CCGGTGATCAAGGCGGCA 62.776 66.667 13.08 0.00 0.00 5.69
153 154 2.044946 AAGCCCGGTGATCAAGGC 60.045 61.111 20.02 20.02 46.13 4.35
154 155 1.452108 GGAAGCCCGGTGATCAAGG 60.452 63.158 10.65 10.65 0.00 3.61
155 156 0.830648 TAGGAAGCCCGGTGATCAAG 59.169 55.000 0.00 0.00 37.58 3.02
156 157 1.416401 GATAGGAAGCCCGGTGATCAA 59.584 52.381 0.00 0.00 37.58 2.57
157 158 1.048601 GATAGGAAGCCCGGTGATCA 58.951 55.000 0.00 0.00 37.58 2.92
158 159 0.038159 CGATAGGAAGCCCGGTGATC 60.038 60.000 0.00 0.00 37.58 2.92
159 160 0.469331 TCGATAGGAAGCCCGGTGAT 60.469 55.000 0.00 0.00 37.58 3.06
160 161 1.076559 TCGATAGGAAGCCCGGTGA 60.077 57.895 0.00 0.00 37.58 4.02
161 162 1.067582 GTCGATAGGAAGCCCGGTG 59.932 63.158 0.00 0.00 37.58 4.94
162 163 2.487532 CGTCGATAGGAAGCCCGGT 61.488 63.158 0.00 0.00 37.58 5.28
163 164 2.335369 CGTCGATAGGAAGCCCGG 59.665 66.667 0.00 0.00 37.58 5.73
164 165 2.335369 CCGTCGATAGGAAGCCCG 59.665 66.667 4.07 0.00 37.58 6.13
165 166 1.807495 CTCCCGTCGATAGGAAGCCC 61.807 65.000 10.96 0.00 0.00 5.19
166 167 1.660917 CTCCCGTCGATAGGAAGCC 59.339 63.158 10.96 0.00 0.00 4.35
167 168 1.660917 CCTCCCGTCGATAGGAAGC 59.339 63.158 10.96 0.00 31.64 3.86
168 169 1.660917 GCCTCCCGTCGATAGGAAG 59.339 63.158 14.80 4.95 31.64 3.46
169 170 1.831286 GGCCTCCCGTCGATAGGAA 60.831 63.158 14.80 0.00 31.64 3.36
170 171 2.203451 GGCCTCCCGTCGATAGGA 60.203 66.667 14.80 8.58 31.64 2.94
171 172 2.520982 TGGCCTCCCGTCGATAGG 60.521 66.667 3.32 8.11 0.00 2.57
172 173 0.536687 TAGTGGCCTCCCGTCGATAG 60.537 60.000 3.32 0.00 0.00 2.08
173 174 0.111832 ATAGTGGCCTCCCGTCGATA 59.888 55.000 3.32 0.00 0.00 2.92
174 175 1.152525 ATAGTGGCCTCCCGTCGAT 60.153 57.895 3.32 0.00 0.00 3.59
175 176 2.125326 CATAGTGGCCTCCCGTCGA 61.125 63.158 3.32 0.00 0.00 4.20
176 177 1.105167 TACATAGTGGCCTCCCGTCG 61.105 60.000 3.32 0.00 0.00 5.12
177 178 1.000955 CATACATAGTGGCCTCCCGTC 59.999 57.143 3.32 0.00 0.00 4.79
178 179 1.048601 CATACATAGTGGCCTCCCGT 58.951 55.000 3.32 0.13 0.00 5.28
179 180 1.273606 CTCATACATAGTGGCCTCCCG 59.726 57.143 3.32 0.00 0.00 5.14
180 181 1.002544 GCTCATACATAGTGGCCTCCC 59.997 57.143 3.32 0.00 0.00 4.30
181 182 1.694150 TGCTCATACATAGTGGCCTCC 59.306 52.381 3.32 0.00 0.00 4.30
182 183 2.548920 GGTGCTCATACATAGTGGCCTC 60.549 54.545 3.32 0.00 0.00 4.70
183 184 1.417890 GGTGCTCATACATAGTGGCCT 59.582 52.381 3.32 0.00 0.00 5.19
184 185 1.873903 CGGTGCTCATACATAGTGGCC 60.874 57.143 0.00 0.00 0.00 5.36
185 186 1.068588 TCGGTGCTCATACATAGTGGC 59.931 52.381 0.00 0.00 0.00 5.01
186 187 3.667497 ATCGGTGCTCATACATAGTGG 57.333 47.619 0.00 0.00 0.00 4.00
187 188 3.990469 GGAATCGGTGCTCATACATAGTG 59.010 47.826 0.00 0.00 0.00 2.74
188 189 3.305403 CGGAATCGGTGCTCATACATAGT 60.305 47.826 0.00 0.00 0.00 2.12
189 190 3.057526 TCGGAATCGGTGCTCATACATAG 60.058 47.826 0.00 0.00 36.95 2.23
190 191 2.888414 TCGGAATCGGTGCTCATACATA 59.112 45.455 0.00 0.00 36.95 2.29
191 192 1.686587 TCGGAATCGGTGCTCATACAT 59.313 47.619 0.00 0.00 36.95 2.29
192 193 1.107945 TCGGAATCGGTGCTCATACA 58.892 50.000 0.00 0.00 36.95 2.29
193 194 2.061773 CATCGGAATCGGTGCTCATAC 58.938 52.381 0.00 0.00 40.82 2.39
194 195 1.000843 CCATCGGAATCGGTGCTCATA 59.999 52.381 0.00 0.00 45.43 2.15
195 196 0.250038 CCATCGGAATCGGTGCTCAT 60.250 55.000 0.00 0.00 45.43 2.90
196 197 1.143838 CCATCGGAATCGGTGCTCA 59.856 57.895 0.00 0.00 45.43 4.26
197 198 1.595382 CCCATCGGAATCGGTGCTC 60.595 63.158 0.00 0.00 45.43 4.26
198 199 2.367202 ACCCATCGGAATCGGTGCT 61.367 57.895 0.00 0.00 45.43 4.40
199 200 2.180204 CACCCATCGGAATCGGTGC 61.180 63.158 8.11 0.00 45.43 5.01
200 201 1.523711 CCACCCATCGGAATCGGTG 60.524 63.158 12.22 12.22 46.27 4.94
201 202 2.908015 CCACCCATCGGAATCGGT 59.092 61.111 0.00 0.00 36.95 4.69
202 203 2.591715 GCCACCCATCGGAATCGG 60.592 66.667 0.00 0.00 36.95 4.18
203 204 2.967076 CGCCACCCATCGGAATCG 60.967 66.667 0.00 0.00 37.82 3.34
204 205 3.279875 GCGCCACCCATCGGAATC 61.280 66.667 0.00 0.00 0.00 2.52
214 215 4.819761 TCATCTGCTCGCGCCACC 62.820 66.667 0.00 0.00 34.43 4.61
215 216 2.176273 AATCATCTGCTCGCGCCAC 61.176 57.895 0.00 0.00 34.43 5.01
216 217 2.175621 CAATCATCTGCTCGCGCCA 61.176 57.895 0.00 0.00 34.43 5.69
217 218 2.630317 CAATCATCTGCTCGCGCC 59.370 61.111 0.00 0.00 34.43 6.53
218 219 2.052414 GCAATCATCTGCTCGCGC 60.052 61.111 0.00 0.00 39.34 6.86
224 225 6.349115 CCATACCAATAAGAGCAATCATCTGC 60.349 42.308 0.00 0.00 42.97 4.26
225 226 6.349115 GCCATACCAATAAGAGCAATCATCTG 60.349 42.308 0.00 0.00 0.00 2.90
226 227 5.709164 GCCATACCAATAAGAGCAATCATCT 59.291 40.000 0.00 0.00 0.00 2.90
227 228 5.709164 AGCCATACCAATAAGAGCAATCATC 59.291 40.000 0.00 0.00 0.00 2.92
228 229 5.638133 AGCCATACCAATAAGAGCAATCAT 58.362 37.500 0.00 0.00 0.00 2.45
229 230 5.052693 AGCCATACCAATAAGAGCAATCA 57.947 39.130 0.00 0.00 0.00 2.57
230 231 4.457257 GGAGCCATACCAATAAGAGCAATC 59.543 45.833 0.00 0.00 0.00 2.67
231 232 4.105377 AGGAGCCATACCAATAAGAGCAAT 59.895 41.667 0.00 0.00 0.00 3.56
232 233 3.459598 AGGAGCCATACCAATAAGAGCAA 59.540 43.478 0.00 0.00 0.00 3.91
233 234 3.048600 AGGAGCCATACCAATAAGAGCA 58.951 45.455 0.00 0.00 0.00 4.26
234 235 3.778954 AGGAGCCATACCAATAAGAGC 57.221 47.619 0.00 0.00 0.00 4.09
235 236 4.322049 CGGTAGGAGCCATACCAATAAGAG 60.322 50.000 13.88 0.00 42.45 2.85
236 237 3.576982 CGGTAGGAGCCATACCAATAAGA 59.423 47.826 13.88 0.00 42.45 2.10
237 238 3.576982 TCGGTAGGAGCCATACCAATAAG 59.423 47.826 13.88 1.25 42.45 1.73
238 239 3.576982 CTCGGTAGGAGCCATACCAATAA 59.423 47.826 13.88 0.00 42.45 1.40
239 240 3.162666 CTCGGTAGGAGCCATACCAATA 58.837 50.000 13.88 1.77 42.45 1.90
240 241 1.971357 CTCGGTAGGAGCCATACCAAT 59.029 52.381 13.88 0.00 42.45 3.16
241 242 1.410004 CTCGGTAGGAGCCATACCAA 58.590 55.000 13.88 0.00 42.45 3.67
242 243 3.127099 CTCGGTAGGAGCCATACCA 57.873 57.895 13.88 3.76 42.45 3.25
252 253 1.481871 TCAACCTTAGCCTCGGTAGG 58.518 55.000 0.00 0.00 46.76 3.18
253 254 2.431057 ACATCAACCTTAGCCTCGGTAG 59.569 50.000 0.00 0.00 32.07 3.18
254 255 2.463752 ACATCAACCTTAGCCTCGGTA 58.536 47.619 0.00 0.00 32.07 4.02
255 256 1.276622 ACATCAACCTTAGCCTCGGT 58.723 50.000 0.00 0.00 34.27 4.69
256 257 2.693591 TCTACATCAACCTTAGCCTCGG 59.306 50.000 0.00 0.00 0.00 4.63
257 258 3.243569 CCTCTACATCAACCTTAGCCTCG 60.244 52.174 0.00 0.00 0.00 4.63
258 259 3.961408 TCCTCTACATCAACCTTAGCCTC 59.039 47.826 0.00 0.00 0.00 4.70
259 260 3.964031 CTCCTCTACATCAACCTTAGCCT 59.036 47.826 0.00 0.00 0.00 4.58
260 261 3.070302 CCTCCTCTACATCAACCTTAGCC 59.930 52.174 0.00 0.00 0.00 3.93
261 262 3.070302 CCCTCCTCTACATCAACCTTAGC 59.930 52.174 0.00 0.00 0.00 3.09
262 263 4.547671 TCCCTCCTCTACATCAACCTTAG 58.452 47.826 0.00 0.00 0.00 2.18
263 264 4.232122 TCTCCCTCCTCTACATCAACCTTA 59.768 45.833 0.00 0.00 0.00 2.69
264 265 3.012959 TCTCCCTCCTCTACATCAACCTT 59.987 47.826 0.00 0.00 0.00 3.50
265 266 2.587777 TCTCCCTCCTCTACATCAACCT 59.412 50.000 0.00 0.00 0.00 3.50
266 267 3.033659 TCTCCCTCCTCTACATCAACC 57.966 52.381 0.00 0.00 0.00 3.77
267 268 4.282496 TCTTCTCCCTCCTCTACATCAAC 58.718 47.826 0.00 0.00 0.00 3.18
268 269 4.541705 CTCTTCTCCCTCCTCTACATCAA 58.458 47.826 0.00 0.00 0.00 2.57
269 270 3.689858 GCTCTTCTCCCTCCTCTACATCA 60.690 52.174 0.00 0.00 0.00 3.07
270 271 2.890945 GCTCTTCTCCCTCCTCTACATC 59.109 54.545 0.00 0.00 0.00 3.06
271 272 2.246067 TGCTCTTCTCCCTCCTCTACAT 59.754 50.000 0.00 0.00 0.00 2.29
272 273 1.641192 TGCTCTTCTCCCTCCTCTACA 59.359 52.381 0.00 0.00 0.00 2.74
273 274 2.092103 TCTGCTCTTCTCCCTCCTCTAC 60.092 54.545 0.00 0.00 0.00 2.59
274 275 2.209758 TCTGCTCTTCTCCCTCCTCTA 58.790 52.381 0.00 0.00 0.00 2.43
275 276 1.006813 TCTGCTCTTCTCCCTCCTCT 58.993 55.000 0.00 0.00 0.00 3.69
276 277 1.756538 CTTCTGCTCTTCTCCCTCCTC 59.243 57.143 0.00 0.00 0.00 3.71
277 278 1.360852 TCTTCTGCTCTTCTCCCTCCT 59.639 52.381 0.00 0.00 0.00 3.69
278 279 1.859302 TCTTCTGCTCTTCTCCCTCC 58.141 55.000 0.00 0.00 0.00 4.30
279 280 3.096092 TCTTCTTCTGCTCTTCTCCCTC 58.904 50.000 0.00 0.00 0.00 4.30
280 281 3.182887 TCTTCTTCTGCTCTTCTCCCT 57.817 47.619 0.00 0.00 0.00 4.20
281 282 3.369366 CCTTCTTCTTCTGCTCTTCTCCC 60.369 52.174 0.00 0.00 0.00 4.30
282 283 3.513515 TCCTTCTTCTTCTGCTCTTCTCC 59.486 47.826 0.00 0.00 0.00 3.71
283 284 4.799564 TCCTTCTTCTTCTGCTCTTCTC 57.200 45.455 0.00 0.00 0.00 2.87
284 285 5.512921 CCTTTCCTTCTTCTTCTGCTCTTCT 60.513 44.000 0.00 0.00 0.00 2.85
285 286 4.694982 CCTTTCCTTCTTCTTCTGCTCTTC 59.305 45.833 0.00 0.00 0.00 2.87
286 287 4.349342 TCCTTTCCTTCTTCTTCTGCTCTT 59.651 41.667 0.00 0.00 0.00 2.85
287 288 3.906846 TCCTTTCCTTCTTCTTCTGCTCT 59.093 43.478 0.00 0.00 0.00 4.09
288 289 4.278975 TCCTTTCCTTCTTCTTCTGCTC 57.721 45.455 0.00 0.00 0.00 4.26
289 290 4.103943 AGTTCCTTTCCTTCTTCTTCTGCT 59.896 41.667 0.00 0.00 0.00 4.24
290 291 4.393834 AGTTCCTTTCCTTCTTCTTCTGC 58.606 43.478 0.00 0.00 0.00 4.26
291 292 6.733145 CAAAGTTCCTTTCCTTCTTCTTCTG 58.267 40.000 0.00 0.00 30.60 3.02
292 293 5.300539 GCAAAGTTCCTTTCCTTCTTCTTCT 59.699 40.000 0.00 0.00 30.60 2.85
293 294 5.524284 GCAAAGTTCCTTTCCTTCTTCTTC 58.476 41.667 0.00 0.00 30.60 2.87
294 295 4.036852 CGCAAAGTTCCTTTCCTTCTTCTT 59.963 41.667 0.00 0.00 30.60 2.52
295 296 3.565902 CGCAAAGTTCCTTTCCTTCTTCT 59.434 43.478 0.00 0.00 30.60 2.85
296 297 3.853676 GCGCAAAGTTCCTTTCCTTCTTC 60.854 47.826 0.30 0.00 30.60 2.87
297 298 2.034685 GCGCAAAGTTCCTTTCCTTCTT 59.965 45.455 0.30 0.00 30.60 2.52
298 299 1.609072 GCGCAAAGTTCCTTTCCTTCT 59.391 47.619 0.30 0.00 30.60 2.85
299 300 1.609072 AGCGCAAAGTTCCTTTCCTTC 59.391 47.619 11.47 0.00 30.60 3.46
300 301 1.692411 AGCGCAAAGTTCCTTTCCTT 58.308 45.000 11.47 0.00 30.60 3.36
301 302 1.692411 AAGCGCAAAGTTCCTTTCCT 58.308 45.000 11.47 0.00 30.60 3.36
302 303 2.127251 CAAAGCGCAAAGTTCCTTTCC 58.873 47.619 11.47 0.00 30.60 3.13
303 304 1.522676 GCAAAGCGCAAAGTTCCTTTC 59.477 47.619 11.47 0.00 41.79 2.62
319 320 2.525075 TGGCATCCACAGGGCAAA 59.475 55.556 0.00 0.00 35.67 3.68
404 407 1.284982 CGTTCTTGCCTGTGGAGTCG 61.285 60.000 0.00 0.00 0.00 4.18
452 455 1.609072 CTCCATCCGCTATCGAAGACA 59.391 52.381 0.00 0.00 42.51 3.41
485 488 3.909430 TCGGTACAAGTAAGCAAGAGTG 58.091 45.455 0.00 0.00 0.00 3.51
1083 1086 2.980568 AGACCAAACTGACGAAACACA 58.019 42.857 0.00 0.00 0.00 3.72
1104 1107 2.679716 GGCTGGTGAGGCTGGAAT 59.320 61.111 0.00 0.00 41.64 3.01
1161 1164 5.047847 GCTTAGTCAATACGGTTCATGCTA 58.952 41.667 0.00 0.00 0.00 3.49
1192 1195 6.899393 AACATTAGCACAATCAAGAAGGAA 57.101 33.333 0.00 0.00 0.00 3.36
1293 1296 3.058501 CACACAAAGATTGAACCGGGTAC 60.059 47.826 6.32 0.00 0.00 3.34
1300 1303 3.988379 TGCTCCACACAAAGATTGAAC 57.012 42.857 0.00 0.00 0.00 3.18
1304 1307 2.555757 GAGCTTGCTCCACACAAAGATT 59.444 45.455 11.24 0.00 0.00 2.40
1404 1407 1.538204 GCGGGCATATCTCAACTCGAA 60.538 52.381 0.00 0.00 0.00 3.71
1456 1459 7.330946 CACTTCGATACATCCTCAAAGTTTACA 59.669 37.037 0.00 0.00 0.00 2.41
1896 1902 4.551388 GTGAGATAACGGGTCTGATGATC 58.449 47.826 0.00 0.00 0.00 2.92
1898 1904 2.693591 GGTGAGATAACGGGTCTGATGA 59.306 50.000 0.00 0.00 0.00 2.92
1957 1964 1.264045 TGACCGCACCCTCATCATCA 61.264 55.000 0.00 0.00 0.00 3.07
2105 2112 3.021269 TCAACATATATGCGGACCGAC 57.979 47.619 20.50 9.82 0.00 4.79
2290 2300 3.134127 GTTCCTGATGCCACGCCC 61.134 66.667 0.00 0.00 0.00 6.13
2300 2310 3.793775 TTTCCGCGCGTGTTCCTGA 62.794 57.895 29.95 14.00 0.00 3.86
2529 2560 2.159254 GGCTGCAAACTGAACTCACAAA 60.159 45.455 0.50 0.00 0.00 2.83
2553 2592 6.963805 GCTAAACTACAGAAACAGATGCAATC 59.036 38.462 0.00 0.00 46.04 2.67
2627 2667 1.302511 CCTAAGTGTTGGGCGCTGT 60.303 57.895 7.64 0.00 38.09 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.